# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 22:00:03 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: N-[(1S)-1-carboxy-3-{[(1S)-1-carboxy-2-(1H-imidazol-5-yl)ethyl]amino}propyl]-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CC[C@H](N[C@@H](CCN[C@@H](Cc1[nH]cnc1)C(O)=O)C(O)=O)C(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 O7J  O7J  'N-[(1S)-1-carboxy-3-{[(1S)-1-carboxy-2-(1H-imidazol-5-yl)ethyl]amino}propyl]-L-glutamic acid'  ligand  45  27  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_O7J
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 O7J  O10   O  OC    -1  -0.626   1.6216   2.6369   3.0907
 O7J  C13   C  CH1    0  -0.148   2.8225   1.0526  -0.5351
 O7J  C14   C  CH2    0  -0.425   3.5939  -0.0279  -1.3005
 O7J  C16   C  C      0   0.412   5.2030  -2.0533  -1.1578
 O7J  C02   C  C      0   0.392  -3.9178   1.5515  -1.1691
 O7J  C04   C  CH1    0  -0.180  -3.4299   0.2189  -0.5451
 O7J  C07   C  CH2    0  -0.448  -0.3254   0.9024   1.4644
 O7J  C08   C  CH1    0  -0.194   1.0907   1.3824   1.1341
 O7J  C09   C  C      0   0.394   1.8692   1.5893   2.4555
 O7J  C15   C  CH2    0  -0.589   4.2832  -1.0607  -0.4214
 O7J  C19   C  C      0   0.387   2.3576   2.1159  -1.5568
 O7J  C22   C  CH2    0  -0.541  -4.6781  -0.5863  -0.1455
 O7J  C23   C  CR5    0   0.357  -4.3743  -1.9116   0.4530
 O7J  C24   C  CR15   0  -0.291  -4.6550  -2.4483   1.6789
 O7J  C26   C  CR15   0   0.069  -3.5902  -3.9596   0.6292
 O7J  N05   N  NH1    0  -0.579  -2.5459   0.3469   0.5908
 O7J  N12   N  NH1    0  -0.601   1.7263   0.4630   0.2073
 O7J  N25   N  N      0  -0.447  -4.1632  -3.7226   1.7796
 O7J  N27   N  NR15   0  -0.614  -3.6945  -2.9000  -0.2011
 O7J  O11   O  O      0  -0.609   2.6482   0.6802   2.8110
 O7J  O17   O  O      0  -0.611   5.5883  -1.7530  -2.3054
 O7J  O18   O  OC    -1  -0.634   5.5116  -3.0868  -0.5259
 O7J  H131  H  HCH1   0   0.154   3.5479   1.5522   0.1319
 O7J  H141  H  HCH2   0   0.195   2.9055  -0.5269  -1.9918
 O7J  H142  H  HCH2   0   0.206   4.3461   0.4666  -1.9170
 O7J  H041  H  HCH1   0   0.203  -2.8929  -0.3414  -1.3201
 O7J  H072  H  HCH2   0   0.204  -0.7597   1.5657   2.2198
 O7J  H071  H  HCH2   0   0.197  -0.2802  -0.0951   1.9168
 O7J  H081  H  HCH1   0   0.202   0.9921   2.3554   0.6449
 O7J  H151  H  HCH2   0   0.218   4.8896  -0.5429   0.3336
 O7J  H152  H  HCH2   0   0.207   3.5550  -1.6428   0.1506
 O7J  H222  H  HCH2   0   0.242  -5.2572  -0.0140   0.5851
 O7J  H221  H  HCH2   0   0.248  -5.3198  -0.7025  -1.0239
 O7J  H241  H  HCR5   0   0.241  -5.1820  -1.9728   2.4929
 O7J  H261  H  HCR5   0   0.269  -3.0894  -4.8712   0.3411
 O7J  H2    H  HNH1   0   0.315  -2.9789   0.9902   1.2454
 O7J  H121  H  HNH1   0   0.326   2.1138  -0.2762   0.7839
 O7J  H271  H  HNR5   0   0.411  -3.3312  -2.8517  -1.1398
 O7J  O20   O  O      0  -0.595   1.2013   2.0433  -2.0109
 O7J  C06   C  CH2    0  -0.235  -1.2320   0.8588   0.2457
 O7J  O01   O  OC    -1  -0.619  -4.2500   1.5124  -2.3715
 O7J  H061  H  HCH2   0   0.172  -1.2629   1.8577  -0.2135
 O7J  H062  H  HCH2   0   0.205  -0.7802   0.2030  -0.5012
 O7J  O21   O  OC    -1  -0.634   3.2258   2.9580  -1.8826
 O7J  O03   O  O      0  -0.607  -3.9885   2.5361  -0.4073

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 O7J  N27  C26   aromatic  1.350  0.020  1.350
 O7J  N27  C23   aromatic  1.366  0.020  1.366
 O7J  C26  N25   aromatic  1.307  0.020  1.307
 O7J  O03  C02   deloc     1.247  0.020  1.247
 O7J  C22  C23   single    1.486  0.020  1.486
 O7J  C22  C04   single    1.538  0.020  1.538
 O7J  C23  C24   aromatic  1.367  0.020  1.367
 O7J  C02  O01   deloc     1.248  0.020  1.248
 O7J  C02  C04   single    1.550  0.020  1.550
 O7J  N25  C24   aromatic  1.370  0.020  1.370
 O7J  C04  N05   single    1.445  0.020  1.445
 O7J  N05  C06   single    1.452  0.020  1.452
 O7J  C06  C07   single    1.520  0.020  1.520
 O7J  O20  C19   deloc     1.244  0.020  1.244
 O7J  O17  C16   deloc     1.247  0.020  1.247
 O7J  C07  C08   single    1.531  0.020  1.531
 O7J  C15  C16   single    1.541  0.020  1.541
 O7J  C15  C14   single    1.521  0.020  1.521
 O7J  C16  O18   deloc     1.250  0.020  1.250
 O7J  N12  C08   single    1.452  0.020  1.452
 O7J  N12  C13   single    1.449  0.020  1.449
 O7J  C19  O21   deloc     1.253  0.020  1.253
 O7J  C19  C13   single    1.546  0.020  1.546
 O7J  C08  C09   single    1.547  0.020  1.547
 O7J  C13  C14   single    1.533  0.020  1.533
 O7J  C09  O11   deloc     1.249  0.020  1.249
 O7J  C09  O10   deloc     1.250  0.020  1.250
 O7J  C13  H131  single    0.970  0.020  1.090
 O7J  C14  H141  single    0.970  0.020  1.090
 O7J  C14  H142  single    0.970  0.020  1.090
 O7J  C04  H041  single    0.970  0.020  1.090
 O7J  C06  H061  single    0.970  0.020  1.090
 O7J  C06  H062  single    0.970  0.020  1.090
 O7J  C07  H072  single    0.970  0.020  1.090
 O7J  C07  H071  single    0.970  0.020  1.090
 O7J  C08  H081  single    0.970  0.020  1.090
 O7J  C15  H151  single    0.970  0.020  1.090
 O7J  C15  H152  single    0.970  0.020  1.090
 O7J  C22  H222  single    0.970  0.020  1.090
 O7J  C22  H221  single    0.970  0.020  1.090
 O7J  C24  H241  single    0.930  0.020  1.080
 O7J  C26  H261  single    0.930  0.020  1.080
 O7J  N05  H2    single    0.890  0.020  1.040
 O7J  N12  H121  single    0.890  0.020  1.040
 O7J  N27  H271  single    0.860  0.020  1.020

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 O7J  H131  C13  N12   111.80  3.000
 O7J  H131  C13  C19   106.58  3.000
 O7J  N12   C13  C19   113.01  3.000
 O7J  H131  C13  C14   106.85  3.000
 O7J  C19   C13  C14   107.83  3.000
 O7J  N12   C13  C14   110.47  3.000
 O7J  H142  C14  H141  106.44  3.000
 O7J  H142  C14  C15   108.77  3.000
 O7J  H141  C14  C15   109.88  3.000
 O7J  H142  C14  C13   108.04  3.000
 O7J  H141  C14  C13   108.66  3.000
 O7J  C15   C14  C13   114.71  3.000
 O7J  O18   C16  O17   126.01  3.000
 O7J  O18   C16  C15   116.01  3.000
 O7J  O17   C16  C15   117.98  3.000
 O7J  O03   C02  O01   126.74  3.000
 O7J  O01   C02  C04   116.40  3.000
 O7J  O03   C02  C04   116.79  3.000
 O7J  H041  C04  N05   107.53  3.000
 O7J  H041  C04  C22   108.27  3.000
 O7J  N05   C04  C22   109.79  3.000
 O7J  H041  C04  C02   107.98  3.000
 O7J  N05   C04  C02   115.65  3.000
 O7J  C22   C04  C02   107.41  3.000
 O7J  H071  C07  H072  106.43  3.000
 O7J  H071  C07  C08   109.64  3.000
 O7J  H072  C07  C08   109.00  3.000
 O7J  H071  C07  C06   109.24  3.000
 O7J  H072  C07  C06   109.51  3.000
 O7J  C08   C07  C06   112.82  3.000
 O7J  H081  C08  N12   108.50  3.000
 O7J  H081  C08  C09   107.96  3.000
 O7J  N12   C08  C09   114.17  3.000
 O7J  H081  C08  C07   106.98  3.000
 O7J  C09   C08  C07   108.84  3.000
 O7J  N12   C08  C07   110.12  3.000
 O7J  O11   C09  C08   117.35  3.000
 O7J  O11   C09  O10   126.08  3.000
 O7J  C08   C09  O10   116.51  3.000
 O7J  H152  C15  H151  105.01  3.000
 O7J  H152  C15  C16   107.73  3.000
 O7J  H151  C15  C16   107.62  3.000
 O7J  H152  C15  C14   111.21  3.000
 O7J  H151  C15  C14   109.11  3.000
 O7J  C16   C15  C14   115.57  3.000
 O7J  O21   C19  O20   126.05  3.000
 O7J  O21   C19  C13   115.20  3.000
 O7J  O20   C19  C13   118.71  3.000
 O7J  H221  C22  H222  106.34  3.000
 O7J  H221  C22  C23   110.40  3.000
 O7J  H222  C22  C23   107.81  3.000
 O7J  H221  C22  C04   108.85  3.000
 O7J  H222  C22  C04   109.22  3.000
 O7J  C23   C22  C04   113.93  3.000
 O7J  N27   C23  C24   104.32  3.000
 O7J  C24   C23  C22   132.02  3.000
 O7J  N27   C23  C22   123.66  3.000
 O7J  H241  C24  N25   121.97  3.000
 O7J  H241  C24  C23   127.09  3.000
 O7J  N25   C24  C23   110.94  3.000
 O7J  H261  C26  N27   122.32  3.000
 O7J  H261  C26  N25   126.27  3.000
 O7J  N27   C26  N25   111.41  3.000
 O7J  H2    N05  C06   108.42  3.000
 O7J  H2    N05  C04   107.59  3.000
 O7J  C06   N05  C04   113.45  3.000
 O7J  H121  N12  C08   105.42  3.000
 O7J  H121  N12  C13   107.38  3.000
 O7J  C08   N12  C13   113.60  3.000
 O7J  C26   N25  C24   105.16  3.000
 O7J  H271  N27  C26   125.63  3.000
 O7J  H271  N27  C23   126.20  3.000
 O7J  C26   N27  C23   108.17  3.000
 O7J  H062  C06  H061  105.76  3.000
 O7J  H062  C06  N05   108.98  3.000
 O7J  H061  C06  N05   113.21  3.000
 O7J  H062  C06  C07   108.60  3.000
 O7J  H061  C06  C07   109.00  3.000
 O7J  N05   C06  C07   111.06  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 O7J  CONST_01  N25   C26  N27  C23     0.00   0.0  0
 O7J  CONST_02  C26   N25  C24  C23     0.00   0.0  0
 O7J  CONST_03  C26   N27  C23  C24     0.00   0.0  0
 O7J  CONST_04  N27   C26  N25  C24     0.00   0.0  0
 O7J  CONST_05  N27   C23  C24  N25     0.00   0.0  0
 O7J  CONST_06  C26   N27  C23  C22   180.00   0.0  0
 O7J  CONST_07  N25   C24  C23  C22   180.00   0.0  0
 O7J  CONST_08  H261  C26  N27  C23   180.00   0.0  0
 O7J  CONST_09  H271  N27  C23  C24   180.00   0.0  0
 O7J  CONST_10  H241  C24  N25  C26   180.00   0.0  0
 O7J  Var_01    N27   C23  C22  C04   -60.53  30.0  2
 O7J  Var_02    C16   C15  C14  C13  -172.86  30.0  2
 O7J  Var_03    O17   C16  C15  C14    18.00  30.0  3
 O7J  Var_04    C07   C06  N05  C04  -177.01  30.0  3
 O7J  Var_05    N05   C06  C07  C08   177.63  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 O7J  chir_01  C13  N12  C19  C14  positiv
 O7J  chir_02  C04  N05  C22  C02  negativ
 O7J  chir_03  C08  N12  C07  C09  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 O7J  plan-1  C22   0.020
 O7J  plan-1  C23   0.020
 O7J  plan-1  C24   0.020
 O7J  plan-1  C26   0.020
 O7J  plan-1  N25   0.020
 O7J  plan-1  N27   0.020
 O7J  plan-1  H241  0.020
 O7J  plan-1  H261  0.020
 O7J  plan-1  H271  0.020
 O7J  plan-2  C16   0.020
 O7J  plan-2  C15   0.020
 O7J  plan-2  O17   0.020
 O7J  plan-2  O18   0.020
 O7J  plan-3  C02   0.020
 O7J  plan-3  C04   0.020
 O7J  plan-3  O01   0.020
 O7J  plan-3  O03   0.020
 O7J  plan-4  O10   0.020
 O7J  plan-4  C08   0.020
 O7J  plan-4  C09   0.020
 O7J  plan-4  O11   0.020
 O7J  plan-5  C13   0.020
 O7J  plan-5  C19   0.020
 O7J  plan-5  O20   0.020
 O7J  plan-5  O21   0.020

